Citrus Sinensis ID: 026355

Local Sequence Feature Prediction

Prediction and (Method)	Result

Residue Number Marker

Protein Sequence

Secondary Structure (PSIPRED)

Secondary Structure Prediction (SSPRO)

Coil and Loop (DISEMBL)

Flexible Loop (DISEMBL)

Low Complexity Region (SEG)

Disordered region (IsUnstruct)

Disordered Region (DISOPRED)

Disordered Region (DISEMBL)

Disordered Region (DISPRO)

Transmembrane Helix (TMHMM)

Transmembrane Helix (HMMTOP)

Transmembrane Helix (MEMSAT)

TM Helix, Signal Peptide (MEMSAT_SVM)

TM Helix, Signal Peptide (Phobius)

Signal Peptide (SignalP HMM Mode)

Signal Peptide (SignalP NN Mode)

Coiled Coils (COILS)

Positional Conservation

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240

MTMLSLNSASWGSASCTKGLQFSPTKIPFGVFKILRARCSSSSSGGNNREPIANYAGVQLEETVDTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGLLVVAKVIFSPFGNHF

ccEEEEcccccccccccccccccccccccHHHHHHHHcccccccccccccccccccccEEEEEEccccccccHHHHHHHccccccHHHHHHHHHcccEEEccEEccccccccccccEEEEEcccccccccccccccccEEEEcccEEEEEcccccEEccccccccHHHHHHHHHHccccccccccccccccccccccccccccccccccccccEEEEcccccccEEEEEccccccccccc

ccEEEEEccccccccccHHHccccccccccHHHHHHHccccccccccccccccccccEEEEEEEcHHHcccHHHHHHHHHcccccHHHHHHHHHcccEEEccEEEcccccEEccccEEEEEccccccccccccccccEEEEEcccEEEEEcccccEEccccccccccHHHHHHHHcccccEEEccccccccccccccccccccccccccccccEEEEEcccccEEEEEEEccHHHHHHcc

mtmlslnsaswgsasctkglqfsptkipfgVFKILRARCsssssggnnrepianyagvqleetvdtKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVshnvkggdmvnctiselqplraeaedipldivyeddnvlvvnkpahmvvhpapgnatgtlvngilhhcslptlassnqeafsdaedisddeefsssisgasirpgivhrldkgtsGLLVVAKVIFSPFGNHF

mtmlslnsaswgsasctkglqfspTKIPFGVFKILRARCSssssggnnrepianYAGVQLEETVDTKAGKLRLDAWissridgisrARVQSSIRSGLVSINGQVVSKVshnvkggdmvNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSssisgasirpgIVHRLDKGTSGLLVVAKVIFSPFGNHF

MTMLSLNSASWGSASCTKGLQFSPTKIPFGVFKILRARCsssssggnnREPIANYAGVQLEETVDTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQeafsdaedisddeefsssisGASIRPGIVHRLDKGTSGLLVVAKVIFSPFGNHF

**************SCTKGLQFSPTKIPFGVFKILRARC*************ANYAGVQLEETVDTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPT******************************RPGIVHRLDKGTSGLLVVAKVIFSPF****

********ASWGSASCTKGLQFSPTKIPFGVF*************************VQLEETVDTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAED************GASIRPGIVHRLDKGTSGLLVVAKVIFS*F****

**************SCTKGLQFSPTKIPFGVFKILRAR********NNREPIANYAGVQLEETVDTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSN******************SISGASIRPGIVHRLDKGTSGLLVVAKVIFSPFGNHF

*TMLSLN*ASWGSASCTKGLQFSPTKIPFGVFKILRARCS*******NREP**NYAGVQLEETVDTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSN****************SSSISGASIRPGIVHRLDKGTSGLLVVAKVIFSPFG**F

oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii

SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooo

xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx

no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Alignment graph	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query		240	2.2.26 [Sep-21-2011]
Q3ECD0		430	RNA pseudourine synthase	no	no	0.75	0.418	0.744	1e-70
Q5Z8P2		445	RNA pseudourine synthase	yes	no	0.733	0.395	0.612	4e-58
Q45480		303	Uncharacterized RNA pseud	yes	no	0.612	0.485	0.430	2e-28
P74346		327	Uncharacterized RNA pseud	N/A	no	0.566	0.415	0.431	8e-28
O50310		327	Uncharacterized RNA pseud	yes	no	0.562	0.412	0.413	6e-27
O67638		316	Uncharacterized RNA pseud	yes	no	0.562	0.427	0.396	3e-26
Q8DEV0		325	Ribosomal large subunit p	yes	no	0.608	0.449	0.401	1e-25
Q87S65		325	Ribosomal large subunit p	yes	no	0.583	0.430	0.386	4e-25
P65836		326	Ribosomal large subunit p	yes	no	0.616	0.453	0.4	4e-25
P65837		326	Ribosomal large subunit p	N/A	no	0.616	0.453	0.4	4e-25

>sp\|Q3ECD0\|PUS2_ARATH RNA pseudourine synthase 2, chloroplastic OS=Arabidopsis thaliana GN=At1g76050 PE=2 SV=1	Back alignment and function desciption

 Score =  266 bits (679), Expect = 1e-70,   Method: Compositional matrix adjust.
 Identities = 137/184 (74%), Positives = 156/184 (84%), Gaps = 4/184 (2%)

Query: 51  PIANYAGVQLEETVDTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSH 110
           P  N AG+++EE VD   GK+RLD+WISSRI+G+SRARVQSSIR GLV++NG+VV KVSH
Sbjct: 62  PRVNNAGLRIEEIVDAAKGKIRLDSWISSRINGVSRARVQSSIRLGLVTVNGRVVDKVSH 121

Query: 111 NVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVN 170
           NVK GD VNCTISELQPL+AEAEDIPLDIVYED +VLVVNKPAHMVVHPAPGN TGTLVN
Sbjct: 122 NVKSGDEVNCTISELQPLKAEAEDIPLDIVYEDKHVLVVNKPAHMVVHPAPGNPTGTLVN 181

Query: 171 GILHHCSLPTLASSN--QEAFSDAEDISDDEEFSSSIS--GASIRPGIVHRLDKGTSGLL 226
           GILHHCSLP +  SN  ++  SD E  SDDEE ++S S   AS+RPGIVHRLDKGT+GLL
Sbjct: 182 GILHHCSLPCVDYSNSEEDDDSDEETFSDDEEMTTSPSSYAASVRPGIVHRLDKGTTGLL 241

Query: 227 VVAK 230
           VVAK
Sbjct: 242 VVAK 245

Arabidopsis thaliana (taxid: 3702)
EC: 5EC: .EC: 4EC: .EC: 9EC: 9EC: .EC: -

>sp\|Q5Z8P2\|PUS2_ORYSJ RNA pseudourine synthase 2, chloroplastic OS=Oryza sativa subsp. japonica GN=Os06g0717400 PE=2 SV=1	Back alignment and function description

>sp\|Q45480\|YLYB_BACSU Uncharacterized RNA pseudouridine synthase YlyB OS=Bacillus subtilis (strain 168) GN=ylyB PE=3 SV=3	Back alignment and function description

>sp\|P74346\|Y1629_SYNY3 Uncharacterized RNA pseudouridine synthase slr1629 OS=Synechocystis sp. (strain PCC 6803 / Kazusa) GN=slr1629 PE=3 SV=1	Back alignment and function description

>sp\|O50310\|Y723_CHLP8 Uncharacterized RNA pseudouridine synthase Cpar_0723 OS=Chlorobaculum parvum (strain NCIB 8327) GN=Cpar_0723 PE=3 SV=1	Back alignment and function description

>sp\|O67638\|Y1758_AQUAE Uncharacterized RNA pseudouridine synthase aq_1758 OS=Aquifex aeolicus (strain VF5) GN=aq_1758 PE=3 SV=1	Back alignment and function description

>sp\|Q8DEV0\|RLUD_VIBVU Ribosomal large subunit pseudouridine synthase D OS=Vibrio vulnificus (strain CMCP6) GN=rluD PE=3 SV=1	Back alignment and function description

>sp\|Q87S65\|RLUD_VIBPA Ribosomal large subunit pseudouridine synthase D OS=Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633) GN=rluD PE=3 SV=1	Back alignment and function description

>sp\|P65836\|RLUD_SALTY Ribosomal large subunit pseudouridine synthase D OS=Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) GN=rluD PE=1 SV=2	Back alignment and function description

>sp\|P65837\|RLUD_SALTI Ribosomal large subunit pseudouridine synthase D OS=Salmonella typhi GN=rluD PE=3 SV=2	Back alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Alignment Graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		240
224065743		444	predicted protein [Populus trichocarpa]	0.916	0.495	0.676	2e-76
449450654		453	PREDICTED: RNA pseudourine synthase 2, c	0.9	0.476	0.644	5e-73
449500428		452	PREDICTED: LOW QUALITY PROTEIN: RNA pseu	0.9	0.477	0.644	6e-73
255556673		399	ribosomal pseudouridine synthase, putati	0.737	0.443	0.773	2e-70
297839485		930	T4O12.25 [Arabidopsis lyrata subsp. lyra	0.75	0.193	0.759	8e-70
42563248		313	RNA pseudourine synthase 2 [Arabidopsis	0.75	0.575	0.744	4e-69
42572121		430	RNA pseudourine synthase 2 [Arabidopsis	0.75	0.418	0.744	6e-69
359492029		433	PREDICTED: RNA pseudourine synthase 2, c	0.925	0.512	0.620	2e-68
357467069		465	RNA pseudourine synthase [Medicago trunc	0.945	0.488	0.571	2e-67
356509084		450	PREDICTED: RNA pseudourine synthase 2, c	0.745	0.397	0.671	4e-66

>gi\|224065743\|ref\|XP_002301949.1\| predicted protein [Populus trichocarpa] gi\|222843675\|gb\|EEE81222.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

 Score =  291 bits (745), Expect = 2e-76,   Method: Compositional matrix adjust.
 Identities = 157/232 (67%), Positives = 183/232 (78%), Gaps = 12/232 (5%)

Query: 3   MLSLNSASWGSASCTKGLQFSPTKIPFGVFKILRARCSSSSSGGNNREP--IANYAGVQL 60
           MLS++S S  SA  +  L   PT       ++L    SS+    +N+ P    NY+GV+L
Sbjct: 30  MLSISSVSRCSAP-SFFLSQKPT-----ASRLLTVHSSSTREPNSNQNPGQRINYSGVKL 83

Query: 61  EETVDTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNC 120
           EE+VD+K+GK RLD+WISSRI GISRARVQSSI+SGLVS+NG+V+ KVSHNVK GD VNC
Sbjct: 84  EESVDSKSGKSRLDSWISSRISGISRARVQSSIKSGLVSVNGKVIDKVSHNVKAGDKVNC 143

Query: 121 TISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPT 180
            ISELQPLRAE E+IPLDIVYED+NVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPT
Sbjct: 144 VISELQPLRAEPENIPLDIVYEDENVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPT 203

Query: 181 LASSNQEAFSDAEDISDDEE--FSSSISGASIRPGIVHRLDKGTSGLLVVAK 230
           ++S  QE  S AED+SDD++    SS   AS+RPGIVHRLDKGTSGLLVVAK
Sbjct: 204 VSS--QEVLSGAEDVSDDDDEGLCSSSYAASVRPGIVHRLDKGTSGLLVVAK 253

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|449450654\|ref\|XP_004143077.1\| PREDICTED: RNA pseudourine synthase 2, chloroplastic-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|449500428\|ref\|XP_004161095.1\| PREDICTED: LOW QUALITY PROTEIN: RNA pseudourine synthase 2, chloroplastic-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|255556673\|ref\|XP_002519370.1\| ribosomal pseudouridine synthase, putative [Ricinus communis] gi\|223541437\|gb\|EEF42987.1\| ribosomal pseudouridine synthase, putative [Ricinus communis]	Back alignment and taxonomy information

>gi\|297839485\|ref\|XP_002887624.1\| T4O12.25 [Arabidopsis lyrata subsp. lyrata] gi\|297333465\|gb\|EFH63883.1\| T4O12.25 [Arabidopsis lyrata subsp. lyrata]	Back alignment and taxonomy information

>gi\|42563248\|ref\|NP_177732.2\| RNA pseudourine synthase 2 [Arabidopsis thaliana] gi\|332197668\|gb\|AEE35789.1\| RNA pseudourine synthase 2 [Arabidopsis thaliana]	Back alignment and taxonomy information

>gi\|42572121\|ref\|NP_974151.1\| RNA pseudourine synthase 2 [Arabidopsis thaliana] gi\|122215273\|sp\|Q3ECD0.1\|PUS2_ARATH RecName: Full=RNA pseudourine synthase 2, chloroplastic; AltName: Full=RNA pseudouridylate synthase 2; AltName: Full=RNA-uridine isomerase 2; Flags: Precursor gi\|332197669\|gb\|AEE35790.1\| RNA pseudourine synthase 2 [Arabidopsis thaliana]	Back alignment and taxonomy information

>gi\|359492029\|ref\|XP_003634352.1\| PREDICTED: RNA pseudourine synthase 2, chloroplastic-like [Vitis vinifera] gi\|302141717\|emb\|CBI18920.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

>gi\|357467069\|ref\|XP_003603819.1\| RNA pseudourine synthase [Medicago truncatula] gi\|355492867\|gb\|AES74070.1\| RNA pseudourine synthase [Medicago truncatula]	Back alignment and taxonomy information

>gi\|356509084\|ref\|XP_003523282.1\| PREDICTED: RNA pseudourine synthase 2, chloroplastic-like [Glycine max]	Back alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Alignment graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		240
TAIR\|locus:2204355		430	AT1G76050 [Arabidopsis thalian	0.75	0.418	0.690	6.2e-62
TIGR_CMR\|CHY_1505		305	CHY_1505 "ribosomal large subu	0.487	0.383	0.411	1.8e-29
TIGR_CMR\|GSU_0082		322	GSU_0082 "ribosomal large subu	0.475	0.354	0.426	1.6e-28
UNIPROTKB\|Q9KU20		324	rluD "Ribosomal large subunit	0.491	0.364	0.393	1.2e-26
TIGR_CMR\|VC_0709		324	VC_0709 "ribosomal large subun	0.491	0.364	0.393	1.2e-26
TIGR_CMR\|SPO_1408		342	SPO_1408 "ribosomal large subu	0.479	0.336	0.432	1.6e-26
UNIPROTKB\|P33643		326	rluD "23S rRNA pseudouridine s	0.487	0.358	0.403	1.9e-26
TIGR_CMR\|CPS_3915		324	CPS_3915 "ribosomal large subu	0.487	0.361	0.403	2.5e-26
UNIPROTKB\|Q4K5V9		320	rluD "Pseudouridine synthase"	0.487	0.365	0.406	6.4e-26
TIGR_CMR\|DET_1375		300	DET_1375 "ribosomal large subu	0.420	0.336	0.392	1.7e-25

TAIR\|locus:2204355 AT1G76050 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 633 (227.9 bits), Expect = 6.2e-62, P = 6.2e-62
 Identities = 127/184 (69%), Positives = 142/184 (77%)

Query:    51 PIANYAGVQLEETVDTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSH 110
             P  N AG+++EE VD   GK+RLD+WISSRI+G+SRARVQSSIR GLV++NG+VV KVSH
Sbjct:    62 PRVNNAGLRIEEIVDAAKGKIRLDSWISSRINGVSRARVQSSIRLGLVTVNGRVVDKVSH 121

Query:   111 NVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVN 170
             NVK GD VNCTISELQPL+AEAEDIPLDIVYED +VLVVNKPAHMVVHPAPGN TGTLVN
Sbjct:   122 NVKSGDEVNCTISELQPLKAEAEDIPLDIVYEDKHVLVVNKPAHMVVHPAPGNPTGTLVN 181

Query:   171 GILHHCSLPTLASSNQXXXXXXXXXXXXX----XXXXXXXGASIRPGIVHRLDKGTSGLL 226
             GILHHCSLP +  SN                          AS+RPGIVHRLDKGT+GLL
Sbjct:   182 GILHHCSLPCVDYSNSEEDDDSDEETFSDDEEMTTSPSSYAASVRPGIVHRLDKGTTGLL 241

Query:   227 VVAK 230
             VVAK
Sbjct:   242 VVAK 245

GO:0001522 "pseudouridine synthesis" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0009451 "RNA modification" evidence=IEA

GO:0009507 "chloroplast" evidence=ISM

GO:0009982 "pseudouridine synthase activity" evidence=IEA;ISS;TAS

TIGR_CMR\|CHY_1505 CHY_1505 "ribosomal large subunit pseudouridine synthase, RluA family" [Carboxydothermus hydrogenoformans Z-2901 (taxid:246194)]	Back alignment and assigned GO terms

TIGR_CMR\|GSU_0082 GSU_0082 "ribosomal large subunit pseudouridine synthase D" [Geobacter sulfurreducens PCA (taxid:243231)]	Back alignment and assigned GO terms

UNIPROTKB\|Q9KU20 rluD "Ribosomal large subunit pseudouridine synthase D" [Vibrio cholerae O1 biovar El Tor str. N16961 (taxid:243277)]	Back alignment and assigned GO terms

TIGR_CMR\|VC_0709 VC_0709 "ribosomal large subunit pseudouridine synthase D" [Vibrio cholerae O1 biovar El Tor (taxid:686)]	Back alignment and assigned GO terms

TIGR_CMR\|SPO_1408 SPO_1408 "ribosomal large subunit pseudouridine synthase D" [Ruegeria pomeroyi DSS-3 (taxid:246200)]	Back alignment and assigned GO terms

UNIPROTKB\|P33643 rluD "23S rRNA pseudouridine synthase" [Escherichia coli K-12 (taxid:83333)]	Back alignment and assigned GO terms

TIGR_CMR\|CPS_3915 CPS_3915 "ribosomal large subunit pseudouridine synthase D" [Colwellia psychrerythraea 34H (taxid:167879)]	Back alignment and assigned GO terms

UNIPROTKB\|Q4K5V9 rluD "Pseudouridine synthase" [Pseudomonas protegens Pf-5 (taxid:220664)]	Back alignment and assigned GO terms

TIGR_CMR\|DET_1375 DET_1375 "ribosomal large subunit pseudouridine synthase, RluA family" [Dehalococcoides ethenogenes 195 (taxid:243164)]	Back alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	5.4.99	LOW CONFIDENCE prediction!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Alignment Graph	Length	Definition	E-value
Query		240
COG0564		289	COG0564, RluA, Pseudouridylate synthases, 23S RNA-	1e-45
TIGR00005		299	TIGR00005, rluA_subfam, pseudouridine synthase, Rl	1e-42
PRK11180		325	PRK11180, rluD, 23S rRNA pseudouridine synthase D;	1e-40
cd02869		185	cd02869, PseudoU_synth_RluCD_like, Pseudouridine s	4e-19
cd00165		70	cd00165, S4, S4/Hsp/ tRNA synthetase RNA-binding d	5e-12
PRK11025		317	PRK11025, PRK11025, 23S rRNA pseudouridylate synth	2e-10
cd02557		213	cd02557, PseudoU_synth_ScRIB2, Pseudouridine synth	8e-10
pfam00849		149	pfam00849, PseudoU_synth_2, RNA pseudouridylate sy	1e-08
smart00363		60	smart00363, S4, S4 RNA-binding domain	2e-08
pfam01479		48	pfam01479, S4, S4 domain	8e-07
COG2302		257	COG2302, COG2302, Uncharacterized conserved protei	2e-06
cd02563		223	cd02563, PseudoU_synth_TruC, tRNA pseudouridine is	6e-06
COG1188		100	COG1188, COG1188, Ribosome-associated heat shock p	1e-05
TIGR03069		257	TIGR03069, PS_II_S4, photosystem II S4 domain prot	4e-05
COG1189		245	COG1189, COG1189, Predicted rRNA methylase [Transl	2e-04
cd02550		154	cd02550, PseudoU_synth_Rsu_Rlu_like, Pseudouridine	4e-04
PRK11112		257	PRK11112, PRK11112, tRNA pseudouridine synthase C;	6e-04
COG1187		248	COG1187, RsuA, 16S rRNA uridine-516 pseudouridylat	8e-04
cd02558		246	cd02558, PSRA_1, Pseudouridine synthase, a subgrou	0.001

>gnl\|CDD\|223638 COG0564, RluA, Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

 Score =  153 bits (389), Expect = 1e-45
 Identities = 73/173 (42%), Positives = 96/173 (55%), Gaps = 32/173 (18%)

Query: 59  QLEETVDTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMV 118
            LE  V  +    RLD +++  +  ISR+R+Q  IR G V +NG+ V K S+ +K GD+V
Sbjct: 1   MLEFEVPEEEAGQRLDKFLAKLL-PISRSRIQKLIRKGRVRVNGKKV-KPSYKLKPGDVV 58

Query: 119 NCTISEL-QPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCS 177
              + E  +  +   EDIPLDI+YED+++LVVNKPA +VVHP  G+  GTLVN +L HC 
Sbjct: 59  RIPLPEEPEEEKLVPEDIPLDILYEDEDLLVVNKPAGLVVHPGGGHHEGTLVNALLRHCQ 118

Query: 178 LPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGLLVVAK 230
                                            RPGIVHRLDK TSGLL+VAK
Sbjct: 119 D-----------------------------GVERPGIVHRLDKDTSGLLLVAK 142

Length = 289

>gnl\|CDD\|161659 TIGR00005, rluA_subfam, pseudouridine synthase, RluA family	Back alignment and domain information

>gnl\|CDD\|183020 PRK11180, rluD, 23S rRNA pseudouridine synthase D; Provisional	Back alignment and domain information

>gnl\|CDD\|211346 cd02869, PseudoU_synth_RluCD_like, Pseudouridine synthase, RsuA/RluD family	Back alignment and domain information

>gnl\|CDD\|238095 cd00165, S4, S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized functional similarity between these three protein classes	Back alignment and domain information

>gnl\|CDD\|182909 PRK11025, PRK11025, 23S rRNA pseudouridylate synthase C; Provisional	Back alignment and domain information

>gnl\|CDD\|211331 cd02557, PseudoU_synth_ScRIB2, Pseudouridine synthases similar to Saccharomyces cerevisiae RIB2	Back alignment and domain information

>gnl\|CDD\|216150 pfam00849, PseudoU_synth_2, RNA pseudouridylate synthase	Back alignment and domain information

>gnl\|CDD\|214638 smart00363, S4, S4 RNA-binding domain	Back alignment and domain information

>gnl\|CDD\|201819 pfam01479, S4, S4 domain	Back alignment and domain information

>gnl\|CDD\|225185 COG2302, COG2302, Uncharacterized conserved protein, contains S4-like domain [Function unknown]	Back alignment and domain information

>gnl\|CDD\|211333 cd02563, PseudoU_synth_TruC, tRNA pseudouridine isomerase C	Back alignment and domain information

>gnl\|CDD\|224109 COG1188, COG1188, Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>gnl\|CDD\|132113 TIGR03069, PS_II_S4, photosystem II S4 domain protein	Back alignment and domain information

>gnl\|CDD\|224110 COG1189, COG1189, Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>gnl\|CDD\|211325 cd02550, PseudoU_synth_Rsu_Rlu_like, Pseudouridine synthase, Rsu/Rlu family	Back alignment and domain information

>gnl\|CDD\|182971 PRK11112, PRK11112, tRNA pseudouridine synthase C; Provisional	Back alignment and domain information

>gnl\|CDD\|224108 COG1187, RsuA, 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>gnl\|CDD\|211332 cd02558, PSRA_1, Pseudouridine synthase, a subgroup of the RluA family	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		240
COG0564		289	RluA Pseudouridylate synthases, 23S RNA-specific [	100.0
PRK11180		325	rluD 23S rRNA pseudouridine synthase D; Provisiona	99.97
TIGR00005		299	rluA_subfam pseudouridine synthase, RluA family. m	99.97
PRK11025		317	23S rRNA pseudouridylate synthase C; Provisional	99.96
PRK10475		290	23S rRNA pseudouridine synthase F; Provisional	99.92
PRK10839		232	16S rRNA pseudouridylate synthase A; Provisional	99.92
PRK10700		289	23S rRNA pseudouridylate synthase B; Provisional	99.9
cd02558		246	PSRA_1 PSRA_1: Pseudouridine synthase, a subgroup	99.88
COG1187		248	RsuA 16S rRNA uridine-516 pseudouridylate synthase	99.87
KOG1919		371	consensus RNA pseudouridylate synthases [RNA proce	99.87
cd02557		213	PseudoU_synth_ScRIB2 PseudoU_synth_ScRIB2_like: Ps	99.75
PRK10158		219	23S rRNA/tRNA pseudouridine synthase A; Provisiona	99.73
TIGR01621		217	RluA-like pseudouridine synthase Rlu family protei	99.7
cd02563		223	PseudoU_synth_TruC tRNA pseudouridine isomerase C:	99.69
PRK11112		257	tRNA pseudouridine synthase C; Provisional	99.68
cd02550		154	PseudoU_synth_Rsu_Rlu_like PseudoU_synth_Rsu_Rlu:	99.58
cd02556		167	PseudoU_synth_RluB PseudoU_synth_RluB: Pseudouridi	99.55
cd02870		146	PseudoU_synth_RsuA_like Pseudouridine synthases ar	99.55
cd02553		167	PseudoU_synth_RsuA PseudoU_synth_RsuA: Pseudouridi	99.5
cd02566		168	PseudoU_synth_RluE PseudoU_synth_RluE: Pseudouridi	99.44
PF00849		164	PseudoU_synth_2: RNA pseudouridylate synthase This	99.43
cd02869		185	PseudoU_synth_RluCD_like PseudoU_synth_RsuA/RluD:	99.39
cd00165		70	S4 S4/Hsp/ tRNA synthetase RNA-binding domain; The	99.36
cd02554		164	PseudoU_synth_RluF PseudoU_synth_RluF_like: Pseudo	99.34
PRK11394		217	23S rRNA pseudouridine synthase E; Provisional	99.33
cd02555		177	PSSA_1 PSSA_1: Pseudouridine synthase, a subgroup	99.32
PF01479		48	S4: S4 domain; InterPro: IPR002942 Ribosomes are t	99.14
TIGR02988		59	YaaA_near_RecF S4 domain protein YaaA. This small	99.08
COG1188		100	Ribosome-associated heat shock protein implicated	98.75
cd02868		226	PseudoU_synth_hTruB2_like PseudoU_synth_ hTRUB2_Li	98.64
smart00363		60	S4 S4 RNA-binding domain.	98.61
PLN00051		267	RNA-binding S4 domain-containing protein; Provisio	98.52
PRK10348		133	ribosome-associated heat shock protein Hsp15; Prov	98.52
TIGR03069		257	PS_II_S4 photosystem II S4 domain protein. Members	98.44
TIGR01017		200	rpsD_bact ribosomal protein S4, bacterial/organell	98.42
CHL00113		201	rps4 ribosomal protein S4; Reviewed	98.38
TIGR00478		228	tly hemolysin TlyA family protein. Hemolysins are	98.23
PRK05327		203	rpsD 30S ribosomal protein S4; Validated	98.22
COG2302		257	Uncharacterized conserved protein, contains S4-lik	98.19
COG0522		205	RpsD Ribosomal protein S4 and related proteins [Tr	98.12
PRK11507		70	ribosome-associated protein; Provisional	98.07
COG1189		245	Predicted rRNA methylase [Translation, ribosomal s	97.95
PF13275		65	S4_2: S4 domain; PDB: 1P9K_A.	97.76
PRK04051		177	rps4p 30S ribosomal protein S4P; Validated	97.65
COG2501		73	S4-like RNA binding protein [Replication, recombin	97.34
PLN00189		194	40S ribosomal protein S9; Provisional	97.18
TIGR01018		162	rpsD_arch ribosomal protein S4(archaeal type)/S9(e	97.05
PTZ00155		181	40S ribosomal protein S9; Provisional	96.89
PRK04313		237	30S ribosomal protein S4e; Validated	96.04
PRK00989		230	truB tRNA pseudouridine synthase B; Provisional	95.86
PLN00036		261	40S ribosomal protein S4; Provisional	95.56
PTZ00223		273	40S ribosomal protein S4; Provisional	95.56
PRK02484		294	truB tRNA pseudouridine synthase B; Provisional	95.52
PTZ00118		262	40S ribosomal protein S4; Provisional	95.48
PRK00020		244	truB tRNA pseudouridine synthase B; Provisional	95.46
PRK14123		305	tRNA pseudouridine synthase B; Provisional	95.4
PRK03287		298	truB tRNA pseudouridine synthase B; Provisional	95.22
PRK14846		345	truB tRNA pseudouridine synthase B; Provisional	95.16
PRK14124		308	tRNA pseudouridine synthase B; Provisional	95.02
PRK05033		312	truB tRNA pseudouridine synthase B; Provisional	95.0
PRK05389		305	truB tRNA pseudouridine synthase B; Provisional	94.88
PRK02755		295	truB tRNA pseudouridine synthase B; Provisional	94.86
PRK01851		303	truB tRNA pseudouridine synthase B; Provisional	94.84
PRK01528		292	truB tRNA pseudouridine synthase B; Provisional	94.83
PRK04270		300	H/ACA RNA-protein complex component Cbf5p; Reviewe	94.47
COG1471		241	RPS4A Ribosomal protein S4E [Translation, ribosoma	93.07
PRK04642		300	truB tRNA pseudouridine synthase B; Provisional	92.91
TIGR00425		322	CBF5 rRNA pseudouridine synthase, putative. This f	92.65
cd02867		312	PseudoU_synth_TruB_4 PseudoU_synth_TruB_4: Pseudou	91.61
PRK13354		410	tyrosyl-tRNA synthetase; Provisional	91.45
PF14451		81	Ub-Mut7C: Mut7-C ubiquitin	90.83
KOG2559		318	consensus Predicted pseudouridine synthase [Transl	90.6
PRK01777		95	hypothetical protein; Validated	90.57
COG0130		271	TruB Pseudouridine synthase [Translation, ribosoma	90.55
COG4332		203	Uncharacterized protein conserved in bacteria [Fun	90.35
PRK05912		408	tyrosyl-tRNA synthetase; Validated	90.23
PF06353		142	DUF1062: Protein of unknown function (DUF1062); In	89.72
PRK08364		70	sulfur carrier protein ThiS; Provisional	84.42
cd00754		80	MoaD Ubiquitin domain of MoaD-like proteins. MoaD	84.39
PRK06437		67	hypothetical protein; Provisional	83.45

>COG0564 RluA Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

Probab=100.00  E-value=1e-33  Score=253.54  Aligned_cols=146  Identities=49%  Similarity=0.710  Sum_probs=128.5

Q ss_pred             EEEEcCCCccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeeeccceecCCCEEEEEeccCC-cccccccCCCcee
Q 026355           61 EETVDTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISELQ-PLRAEAEDIPLDI  139 (240)
Q Consensus        61 ~~~V~~~~~g~RLdk~L~~~~~~~SR~~~~klI~~G~V~VNG~~v~~~~~~L~~GD~I~v~~~~~~-~~~~~p~~~~l~I  139 (240)
                      ++.|....+++|||+||++.++ +||+.+++++++|+|.|||+++. ++++|+.||+|.+...+.. .....+++++++|
T Consensus         3 ~~~v~~~~~g~rld~~L~~l~~-~sr~~~~~~i~~g~v~vNg~~v~-~~~~l~~gd~i~~~~~~~~~~~~~~~~~~~l~I   80 (289)
T COG0564           3 EFEVPEEEAGQRLDKFLAKLLP-ISRSRIQKLIRKGRVRVNGKKVK-PSYKLKPGDVVRIPLPEEPEEEKLVPEDIPLDI   80 (289)
T ss_pred             eEEeChhhcCCCHHHHHHHccC-cCHHHHHHHHHCCCEEECCEEcc-CCeeeCCCCEEEEecccccccccccccCCCccE
Confidence            4567778899999999999655 99999999999999999999996 9999999999999887644 3445667778999


Q ss_pred             eecCCcEEEEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccCcCC
Q 026355          140 VYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLD  219 (240)
Q Consensus       140 lyed~~~lvvnKPaGl~v~p~~~~~~~Tl~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~VhRLD  219 (240)
                      ||||++++|||||+||+|||++++..+|++++|+.++...                             ..++++|||||
T Consensus        81 lyED~~llVvnKP~Gl~vhp~~~~~~~tl~~~l~~~~~~~-----------------------------~~~~~~vHRLD  131 (289)
T COG0564          81 LYEDEDLLVVNKPAGLVVHPGGGHHEGTLVNALLRHCQDG-----------------------------VERPGIVHRLD  131 (289)
T ss_pred             EEecCCEEEEECCCCCcCcCCCCCccHhHHHHHHHhcccc-----------------------------CCceeeeccCC
Confidence            9999999999999999999999999999999999986310                             26788999999


Q ss_pred             CCCceEEEeecCCccccC
Q 026355          220 KGTSGLLVVAKVIFSPFG  237 (240)
Q Consensus       220 r~TSGLLl~ak~~~aa~~  237 (240)
                      |+||||||+||+..++..
T Consensus       132 kdTSGlll~AK~~~a~~~  149 (289)
T COG0564         132 KDTSGLLLVAKNREAARE  149 (289)
T ss_pred             CCCceEEEEECCHHHHHH
Confidence            999999999999987754

>PRK11180 rluD 23S rRNA pseudouridine synthase D; Provisional	Back alignment and domain information

>TIGR00005 rluA_subfam pseudouridine synthase, RluA family	Back alignment and domain information

>PRK11025 23S rRNA pseudouridylate synthase C; Provisional	Back alignment and domain information

>PRK10475 23S rRNA pseudouridine synthase F; Provisional	Back alignment and domain information

>PRK10839 16S rRNA pseudouridylate synthase A; Provisional	Back alignment and domain information

>PRK10700 23S rRNA pseudouridylate synthase B; Provisional	Back alignment and domain information

>cd02558 PSRA_1 PSRA_1: Pseudouridine synthase, a subgroup of the RluA family	Back alignment and domain information

>COG1187 RsuA 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>KOG1919 consensus RNA pseudouridylate synthases [RNA processing and modification]	Back alignment and domain information

>cd02557 PseudoU_synth_ScRIB2 PseudoU_synth_ScRIB2_like: Pseudouridine synthase, Saccharomyces cerevisiae RIB2_like	Back alignment and domain information

>PRK10158 23S rRNA/tRNA pseudouridine synthase A; Provisional	Back alignment and domain information

>TIGR01621 RluA-like pseudouridine synthase Rlu family protein, TIGR01621	Back alignment and domain information

>cd02563 PseudoU_synth_TruC tRNA pseudouridine isomerase C: Pseudouridine synthases catalyze the isomerization of specific uridines in an tRNA molecule to pseudouridines (5-ribosyluracil, psi)	Back alignment and domain information

>PRK11112 tRNA pseudouridine synthase C; Provisional	Back alignment and domain information

>cd02550 PseudoU_synth_Rsu_Rlu_like PseudoU_synth_Rsu_Rlu: Pseudouridine synthase, Rsu/Rlu family	Back alignment and domain information

>cd02556 PseudoU_synth_RluB PseudoU_synth_RluB: Pseudouridine synthase, Escherichia coli RluB like	Back alignment and domain information

>cd02870 PseudoU_synth_RsuA_like Pseudouridine synthases are responsible for the synthesis of pseudouridine from uracil in ribosomal RNA	Back alignment and domain information

>cd02553 PseudoU_synth_RsuA PseudoU_synth_RsuA: Pseudouridine synthase, Escherichia coli RsuA like	Back alignment and domain information

>cd02566 PseudoU_synth_RluE PseudoU_synth_RluE: Pseudouridine synthase, Escherichia coli RluE	Back alignment and domain information

>PF00849 PseudoU_synth_2: RNA pseudouridylate synthase This Prosite family is a subset of the Pfam family	Back alignment and domain information

>cd02869 PseudoU_synth_RluCD_like PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family	Back alignment and domain information

>cd00165 S4 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized functional similarity between these three protein classes	Back alignment and domain information

>cd02554 PseudoU_synth_RluF PseudoU_synth_RluF_like: Pseudouridine synthase, Escherichia coli RluF like	Back alignment and domain information

>PRK11394 23S rRNA pseudouridine synthase E; Provisional	Back alignment and domain information

>cd02555 PSSA_1 PSSA_1: Pseudouridine synthase, a subgroup of the RsuA family	Back alignment and domain information

>PF01479 S4: S4 domain; InterPro: IPR002942 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms	Back alignment and domain information

>TIGR02988 YaaA_near_RecF S4 domain protein YaaA	Back alignment and domain information

>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>cd02868 PseudoU_synth_hTruB2_like PseudoU_synth_ hTRUB2_Like: Pseudouridine synthase, humanTRUB2_like	Back alignment and domain information

>smart00363 S4 S4 RNA-binding domain	Back alignment and domain information

>PLN00051 RNA-binding S4 domain-containing protein; Provisional	Back alignment and domain information

>PRK10348 ribosome-associated heat shock protein Hsp15; Provisional	Back alignment and domain information

>TIGR03069 PS_II_S4 photosystem II S4 domain protein	Back alignment and domain information

>TIGR01017 rpsD_bact ribosomal protein S4, bacterial/organelle type	Back alignment and domain information

>CHL00113 rps4 ribosomal protein S4; Reviewed	Back alignment and domain information

>TIGR00478 tly hemolysin TlyA family protein	Back alignment and domain information

>PRK05327 rpsD 30S ribosomal protein S4; Validated	Back alignment and domain information

>COG2302 Uncharacterized conserved protein, contains S4-like domain [Function unknown]	Back alignment and domain information

>COG0522 RpsD Ribosomal protein S4 and related proteins [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>PRK11507 ribosome-associated protein; Provisional	Back alignment and domain information

>COG1189 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>PF13275 S4_2: S4 domain; PDB: 1P9K_A	Back alignment and domain information

>PRK04051 rps4p 30S ribosomal protein S4P; Validated	Back alignment and domain information

>COG2501 S4-like RNA binding protein [Replication, recombination, and repair]	Back alignment and domain information

>PLN00189 40S ribosomal protein S9; Provisional	Back alignment and domain information

>TIGR01018 rpsD_arch ribosomal protein S4(archaeal type)/S9(eukaryote cytosolic type)	Back alignment and domain information

>PTZ00155 40S ribosomal protein S9; Provisional	Back alignment and domain information

>PRK04313 30S ribosomal protein S4e; Validated	Back alignment and domain information

>PRK00989 truB tRNA pseudouridine synthase B; Provisional	Back alignment and domain information

>PLN00036 40S ribosomal protein S4; Provisional	Back alignment and domain information

>PTZ00223 40S ribosomal protein S4; Provisional	Back alignment and domain information

>PRK02484 truB tRNA pseudouridine synthase B; Provisional	Back alignment and domain information

>PTZ00118 40S ribosomal protein S4; Provisional	Back alignment and domain information

>PRK00020 truB tRNA pseudouridine synthase B; Provisional	Back alignment and domain information

>PRK14123 tRNA pseudouridine synthase B; Provisional	Back alignment and domain information

>PRK03287 truB tRNA pseudouridine synthase B; Provisional	Back alignment and domain information

>PRK14846 truB tRNA pseudouridine synthase B; Provisional	Back alignment and domain information

>PRK14124 tRNA pseudouridine synthase B; Provisional	Back alignment and domain information

>PRK05033 truB tRNA pseudouridine synthase B; Provisional	Back alignment and domain information

>PRK05389 truB tRNA pseudouridine synthase B; Provisional	Back alignment and domain information

>PRK02755 truB tRNA pseudouridine synthase B; Provisional	Back alignment and domain information

>PRK01851 truB tRNA pseudouridine synthase B; Provisional	Back alignment and domain information

>PRK01528 truB tRNA pseudouridine synthase B; Provisional	Back alignment and domain information

>PRK04270 H/ACA RNA-protein complex component Cbf5p; Reviewed	Back alignment and domain information

>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>PRK04642 truB tRNA pseudouridine synthase B; Provisional	Back alignment and domain information

>TIGR00425 CBF5 rRNA pseudouridine synthase, putative	Back alignment and domain information

>cd02867 PseudoU_synth_TruB_4 PseudoU_synth_TruB_4: Pseudouridine synthase homolog 4	Back alignment and domain information

>PRK13354 tyrosyl-tRNA synthetase; Provisional	Back alignment and domain information

>PF14451 Ub-Mut7C: Mut7-C ubiquitin	Back alignment and domain information

>KOG2559 consensus Predicted pseudouridine synthase [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>PRK01777 hypothetical protein; Validated	Back alignment and domain information

>COG0130 TruB Pseudouridine synthase [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>COG4332 Uncharacterized protein conserved in bacteria [Function unknown]	Back alignment and domain information

>PRK05912 tyrosyl-tRNA synthetase; Validated	Back alignment and domain information

>PF06353 DUF1062: Protein of unknown function (DUF1062); InterPro: IPR009412 This entry consists of several hypothetical bacterial proteins of unknown function	Back alignment and domain information

>PRK08364 sulfur carrier protein ThiS; Provisional	Back alignment and domain information

>cd00754 MoaD Ubiquitin domain of MoaD-like proteins	Back alignment and domain information

>PRK06437 hypothetical protein; Provisional	Back alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Alignment Graph	Length	Definition	E-value
Query		240
1v9f_A		325	Crystal Structure Of Catalytic Domain Of Pseudourid		3e-24
1qyu_A		349	Structure Of The Catalytic Domain Of 23s Rrna Pseud		7e-24
1prz_A		252	Crystal Structure Of Pseudouridine Synthase Rlud Ca		5e-16

>pdb|1V9F|A Chain A, Crystal Structure Of Catalytic Domain Of Pseudouridine Synthase Rlud From Escherichia Coli Length = 325

Back alignment and structure

Iteration: 1

Score = 108 bits (270), Expect = 3e-24, Method: Compositional matrix adjust. Identities = 65/175 (37%), Positives = 90/175 (51%), Gaps = 27/175 (15%) Query: 58 VQLEETVDTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDM 117 VQL TV RLD ++ SR+R++ I V +NG+V K V GG+ Sbjct: 4 VQLTATVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQ 63 Query: 118 VNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCS 177 V + R E +DIPLDIVYED++++++NKP +VVHP GN GT++N +LH+ Sbjct: 64 VAINAEIEEEARFEPQDIPLDIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLNALLHYY- 122 Query: 178 LPTLASSNQXXXXXXXXXXXXXXXXXXXXGASIRPGIVHRLDKGTSGLLVVAKVI 232 P +A R GIVHRLDK T+GL+VVAK + Sbjct: 123 -PPIADVP-------------------------RAGIVHRLDKDTTGLMVVAKTV 151

PyMOL of 1v9f

>pdb|1QYU|A Chain A, Structure Of The Catalytic Domain Of 23s Rrna Pseudouridine Synthase Rlud Length = 349

Back alignment and structure

>pdb|1PRZ|A Chain A, Crystal Structure Of Pseudouridine Synthase Rlud Catalytic Module Length = 252

Back alignment and structure

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		240
1v9f_A		325	Ribosomal large subunit pseudouridine synthase D;	1e-72
2i82_A		217	Ribosomal large subunit pseudouridine synthase A;	1e-36
1v9k_A		228	Ribosomal large subunit pseudouridine synthase C;	2e-30
2k6p_A		92	Uncharacterized protein HP_1423; alpha-L motif, RN	1e-09
1dm9_A		133	Hypothetical 15.5 KD protein in MRCA-PCKA intergen	5e-06
1vio_A		243	Ribosomal small subunit pseudouridine synthase A;	8e-04

>1v9f_A Ribosomal large subunit pseudouridine synthase D; RNA binding, lyase; 1.70A {Escherichia coli} SCOP: d.265.1.3 PDB: 2ist_A 1qyu_A 1prz_A Length = 325	Back alignment and structure

 Score =  223 bits (570), Expect = 1e-72
 Identities = 64/173 (36%), Positives = 88/173 (50%), Gaps = 27/173 (15%)

Query: 58  VQLEETVDTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDM 117
           VQL  TV       RLD  ++      SR+R++  I    V +NG+V  K    V GG+ 
Sbjct: 4   VQLTATVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQ 63

Query: 118 VNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCS 177
           V       +  R E +DIPLDIVYED++++++NKP  +VVHP  GN  GT++N +LH+  
Sbjct: 64  VAINAEIEEEARFEPQDIPLDIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLNALLHYY- 122

Query: 178 LPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGLLVVAK 230
                                      I+    R GIVHRLDK T+GL+VVAK
Sbjct: 123 -------------------------PPIAD-VPRAGIVHRLDKDTTGLMVVAK 149

PyMOL of 1v9f

>2i82_A Ribosomal large subunit pseudouridine synthase A; lyase/RNA complex; HET: FOU; 2.05A {Escherichia coli} Length = 217	Back alignment and structure

>1v9k_A Ribosomal large subunit pseudouridine synthase C; pseudouridine syntase, RNA binding, lyase; 2.00A {Escherichia coli} SCOP: d.265.1.3 PDB: 1xpi_A Length = 228	Back alignment and structure

>2k6p_A Uncharacterized protein HP_1423; alpha-L motif, RNA-binding, unknown function; NMR {Helicobacter pylori} Length = 92	Back alignment and structure

>1dm9_A Hypothetical 15.5 KD protein in MRCA-PCKA intergenic region; heat shock proteins, protein-RNA interactions, ribosome, structural genomics; 2.00A {Escherichia coli} SCOP: d.66.1.3 PDB: 3bbu_A Length = 133	Back alignment and structure

>1vio_A Ribosomal small subunit pseudouridine synthase A; structural genomics, lyase; 1.59A {Haemophilus influenzae} SCOP: d.265.1.3 d.66.1.5 Length = 243	Back alignment and structure

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		240
1v9f_A		325	Ribosomal large subunit pseudouridine synthase D;	99.97
1ksk_A		234	Ribosomal small subunit pseudouridine synthase A;	99.95
1vio_A		243	Ribosomal small subunit pseudouridine synthase A;	99.95
3dh3_A		290	Ribosomal large subunit pseudouridine synthase F;	99.94
2i82_A		217	Ribosomal large subunit pseudouridine synthase A;	99.75
2oml_A		189	Ribosomal large subunit pseudouridine synthase E;	99.72
2olw_A		217	Ribosomal large subunit pseudouridine synthase E;	99.71
1v9k_A		228	Ribosomal large subunit pseudouridine synthase C;	99.69
2gml_A		237	Ribosomal large subunit pseudouridine synthase F;	99.46
2k6p_A		92	Uncharacterized protein HP_1423; alpha-L motif, RN	99.02
1dm9_A		133	Hypothetical 15.5 KD protein in MRCA-PCKA intergen	98.97
1c05_A		159	Ribosomal protein S4 delta 41; two subdomains, uni	98.8
2vqe_D		209	30S ribosomal protein S4; tRNA-binding, rRNA-bindi	98.76
1p9k_A		79	ORF, hypothetical protein; alfal motif, RNA-bindin	98.75
2cqj_A		71	BRMS2, U3 small nucleolar ribonucleoprotein protei	98.57
3r8n_D		205	30S ribosomal protein S4; protein biosynthesis, RN	98.42
3hp7_A		291	Hemolysin, putative; structural genomics, APC64019	98.39
3bbn_D		201	Ribosomal protein S4; small ribosomal subunit, spi	98.39
3j20_D		180	30S ribosomal protein S4P; archaea, archaeal, KINK	98.2
2xzm_D		181	Ribosomal protein S4 containing protein; ribosome,	98.14
3u5c_J		197	40S ribosomal protein S9-A; translation, ribosome,	97.92
3iz6_C		195	40S ribosomal protein S9 (S4P); eukaryotic ribosom	97.42
3j20_E		243	30S ribosomal protein S4E; archaea, archaeal, KINK	97.07
3kbg_A		213	30S ribosomal protein S4E; RPS4E, RS4E_theac, TAR2	96.88
1r3e_A		309	TRNA pseudouridine synthase B; RNA modification, p	95.15
1sgv_A		316	TRNA pseudouridine synthase B; hinged motion, tRNA	94.9
1k8w_A		327	TRNA pseudouridine synthase B; protein-RNA complex	94.87
2aus_C		334	Pseudouridine synthase; isomerase, structural prot	94.82
2xzm_W		260	40S ribosomal protein S4; ribosome, translation; 3	94.38
2apo_A		357	Probable tRNA pseudouridine synthase B; protein-pr	94.29
3iz6_D		265	40S ribosomal protein S4 (S4E); eukaryotic ribosom	94.15
3u28_A		400	H/ACA ribonucleoprotein complex subunit 4; pseudou	93.68
3u5c_E		261	RP5, S7, YS6, 40S ribosomal protein S4-A; translat	93.61
1jil_A		420	Tyrrs, tyrosyl-tRNA synthetase; truncation, based	92.89
1h3f_A		432	Tyrosyl-tRNA synthetase; ligase, aminoacyl-tRNA sy	92.5
1fm0_D		81	Molybdopterin convertin factor, subunit 1; molybde	90.42
2ktl_A		164	Tyrosyl-tRNA synthetase; S4 fold, aminoacyl-tRNA s	90.14
2jan_A		432	Tyrosyl-tRNA synthetase; protein biosynthesis, ami	90.11
2ts1_A		419	Tyrosyl-tRNA synthetase; ligase (synthetase); 2.30	87.4

>1v9f_A Ribosomal large subunit pseudouridine synthase D; RNA binding, lyase; 1.70A {Escherichia coli} SCOP: d.265.1.3 PDB: 2ist_A 1qyu_A 1prz_A	Back alignment and structure

Probab=99.97  E-value=1.3e-32  Score=248.74  Aligned_cols=151  Identities=40%  Similarity=0.606  Sum_probs=67.3

Q ss_pred             EEEEEcCCCccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeeeccceecCCCEEEEEeccCCcccccccCCCcee
Q 026355           60 LEETVDTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISELQPLRAEAEDIPLDI  139 (240)
Q Consensus        60 ~~~~V~~~~~g~RLdk~L~~~~~~~SR~~~~klI~~G~V~VNG~~v~~~~~~L~~GD~I~v~~~~~~~~~~~p~~~~l~I  139 (240)
                      ++++|+..++++|||+||++.++.+||+.++++|++|+|+|||+++.+++++|++||+|++.....++....++.+++.|
T Consensus         6 ~~~~v~~~~~g~RLd~~L~~~~~~~SR~~~~~lI~~G~V~VNG~~v~~~~~~v~~gD~I~v~~~~~~~~~~~~~~~~~~i   85 (325)
T 1v9f_A            6 LTATVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINAEIEEEARFEPQDIPLDI   85 (325)
T ss_dssp             ----------------------------------------------------------------------CCCCCCCCCE
T ss_pred             EEEEECCccCCchHHHHHHhhccccCHHHHHHHHHCCCEEECCEEccCCCCEeCCCCEEEEeccccccccCCcccCCCeE
Confidence            45678888899999999999876799999999999999999999966899999999999998764433334456677899


Q ss_pred             eecCCcEEEEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccCcCC
Q 026355          140 VYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLD  219 (240)
Q Consensus       140 lyed~~~lvvnKPaGl~v~p~~~~~~~Tl~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~VhRLD  219 (240)
                      +|||++++|+|||+||+|||++++..+|+++.|..++...                           ....++++|||||
T Consensus        86 lyed~~~lvvnKP~G~~~~~~~~~~~~tl~~~l~~~~~~~---------------------------~~~~~~~~vhRLD  138 (325)
T 1v9f_A           86 VYEDEDIIIINKPRDLVVHPGAGNPDGTVLNALLHYYPPI---------------------------ADVPRAGIVHRLD  138 (325)
T ss_dssp             EEECSSEEEEEECSSCCSSCBTTBSSSSHHHHHHHHCGGG---------------------------GGSGGGGBCCCCC
T ss_pred             EEECCCEEEEECCCCCeEecCCCCCCccHHHHHHHHHHhc---------------------------CCCCceeeecCCC
Confidence            9999999999999999999998887889999998876210                           0113578899999


Q ss_pred             CCCceEEEeecCCccccC
Q 026355          220 KGTSGLLVVAKVIFSPFG  237 (240)
Q Consensus       220 r~TSGLLl~ak~~~aa~~  237 (240)
                      ++||||||||||+++++.
T Consensus       139 ~~TSGlll~ak~~~~~~~  156 (325)
T 1v9f_A          139 KDTTGLMVVAKTVPAQTR  156 (325)
T ss_dssp             TTCEEEEEEESSHHHHHH
T ss_pred             CCCeeEEEEEcCHHHHHH
Confidence            999999999999987653

PyMOL of 1v9f

>1ksk_A Ribosomal small subunit pseudouridine synthase A; RSUA, lyase; 2.00A {Escherichia coli} SCOP: d.265.1.3 d.66.1.5 PDB: 1ksl_A 1ksv_A*	Back alignment and structure

>1vio_A Ribosomal small subunit pseudouridine synthase A; structural genomics, lyase; 1.59A {Haemophilus influenzae} SCOP: d.265.1.3 d.66.1.5	Back alignment and structure

>3dh3_A Ribosomal large subunit pseudouridine synthase F; protein-RNA complex, S4 domain, alpha/beta protein, isomerase, RNA-binding, rRNA processing; HET: FHU; 3.00A {Escherichia coli}	Back alignment and structure

>2i82_A Ribosomal large subunit pseudouridine synthase A; lyase/RNA complex; HET: FOU; 2.05A {Escherichia coli}	Back alignment and structure

>2oml_A Ribosomal large subunit pseudouridine synthase E; bifurcated beta sheet, thrombin-cleaved, isomerase; 1.20A {Escherichia coli}	Back alignment and structure

>2olw_A Ribosomal large subunit pseudouridine synthase E; bifurcated beta sheet, isomerase; 1.60A {Escherichia coli}	Back alignment and structure

>1v9k_A Ribosomal large subunit pseudouridine synthase C; pseudouridine syntase, RNA binding, lyase; 2.00A {Escherichia coli} SCOP: d.265.1.3 PDB: 1xpi_A	Back alignment and structure

>2gml_A Ribosomal large subunit pseudouridine synthase F; RLUF, ribosome, RNA modifying enzyme, isomerase; 2.60A {Escherichia coli}	Back alignment and structure

>2k6p_A Uncharacterized protein HP_1423; alpha-L motif, RNA-binding, unknown function; NMR {Helicobacter pylori}	Back alignment and structure

>1dm9_A Hypothetical 15.5 KD protein in MRCA-PCKA intergenic region; heat shock proteins, protein-RNA interactions, ribosome, structural genomics; 2.00A {Escherichia coli} SCOP: d.66.1.3 PDB: 3bbu_A	Back alignment and structure

>1c05_A Ribosomal protein S4 delta 41; two subdomains, unique topology, possible helix-turn-helix motif, ribosome; NMR {Geobacillus stearothermophilus} SCOP: d.66.1.2 PDB: 1c06_A 1eg0_A 1qd7_C	Back alignment and structure

>2vqe_D 30S ribosomal protein S4; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} SCOP: d.66.1.2 PDB: 1hnw_D* 1hnx_D* 1hnz_D* 1ibk_D* 1fka_D* 1ibm_D 1xmo_D* 1ibl_D* 1xnq_D* 1xnr_D* 1yl4_G 2b64_D* 2b9m_D* 2b9o_D* 2hgi_G 2hgp_G 2hgr_G 2hhh_D* 1xmq_D* 2j02_D* ...	Back alignment and structure

>1p9k_A ORF, hypothetical protein; alfal motif, RNA-binding protein, E.coli, montreal-kingston structural genomics initiative, BSGI; NMR {Escherichia coli} SCOP: d.66.1.6	Back alignment and structure

>2cqj_A BRMS2, U3 small nucleolar ribonucleoprotein protein IMP3 homolog; S4 domain, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>3hp7_A Hemolysin, putative; structural genomics, APC64019, PSI-2, protein STR initiative, midwest center for structural genomics, MCSG; HET: MSE; 1.53A {Streptococcus thermophilus}	Back alignment and structure

>3bbn_D Ribosomal protein S4; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea}	Back alignment and structure

>3j20_D 30S ribosomal protein S4P; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}	Back alignment and structure

>2xzm_D Ribosomal protein S4 containing protein; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_D	Back alignment and structure

>3u5c_J 40S ribosomal protein S9-A; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3izb_C 3o30_E 3o2z_E 3u5g_J 1s1h_D 3jyv_D*	Back alignment and structure

>3iz6_C 40S ribosomal protein S9 (S4P); eukaryotic ribosome,homology modeling,de novo modeling,ribos proteins,novel ribosomal proteins, ribosome; 5.50A {Triticum aestivum}	Back alignment and structure

>3j20_E 30S ribosomal protein S4E; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}	Back alignment and structure

>3kbg_A 30S ribosomal protein S4E; RPS4E, RS4E_theac, TAR28, NESG, structural genomics, PSI-2, protein structure initiative; HET: MSE; 1.75A {Thermoplasma acidophilum}	Back alignment and structure

>1r3e_A TRNA pseudouridine synthase B; RNA modification, pseudouridylation, lyase-RNA complex; HET: FHU; 2.10A {Thermotoga maritima} SCOP: b.122.1.1 d.265.1.2 PDB: 1ze2_A* 2ab4_A* 1ze1_A	Back alignment and structure

>1sgv_A TRNA pseudouridine synthase B; hinged motion, tRNA modification, structural genomics, PSI, structure initiative; 1.90A {Mycobacterium tuberculosis} SCOP: b.122.1.1 d.265.1.2	Back alignment and structure

>1k8w_A TRNA pseudouridine synthase B; protein-RNA complex, T stem-loop, lyase/RNA complex; HET: FHU; 1.85A {Escherichia coli} SCOP: b.122.1.1 d.265.1.2 PDB: 1zl3_A* 1r3f_A	Back alignment and structure

>2aus_C Pseudouridine synthase; isomerase, structural protein, isomerase-structural protein; 2.10A {Pyrococcus abyssi} PDB: 3lwr_A 3lwo_A* 3lwq_A* 3lwp_A 3lwv_A 3hax_A* 2hvy_A* 3hay_A* 2ey4_A 2rfk_A 3mqk_A 3hjw_A* 3hjy_A	Back alignment and structure

>2xzm_W 40S ribosomal protein S4; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_W	Back alignment and structure

>2apo_A Probable tRNA pseudouridine synthase B; protein-protein complex, box H/ACA, snoRNP, pseudouridine synthase, RNA modification; 1.95A {Methanocaldococcus jannaschii} SCOP: b.122.1.1 d.265.1.2	Back alignment and structure

>3iz6_D 40S ribosomal protein S4 (S4E); eukaryotic ribosome,homology modeling,de novo modeling,ribos proteins,novel ribosomal proteins, ribosome; 5.50A {Triticum aestivum}	Back alignment and structure

>3u28_A H/ACA ribonucleoprotein complex subunit 4; pseudouridine synthase, pseudouridylation, H/ACA RNA; 1.90A {Saccharomyces cerevisiae} PDB: 3uai_A	Back alignment and structure

>3u5c_E RP5, S7, YS6, 40S ribosomal protein S4-A; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3izb_D 3u5g_E	Back alignment and structure

>1jil_A Tyrrs, tyrosyl-tRNA synthetase; truncation, based inhibitor design, ligase; HET: 485; 2.20A {Staphylococcus aureus} SCOP: c.26.1.1 PDB: 1jij_A* 1jii_A* 1jik_A*	Back alignment and structure

>1h3f_A Tyrosyl-tRNA synthetase; ligase, aminoacyl-tRNA synthetase; HET: TYE; 2.00A {Thermus thermophilus} SCOP: c.26.1.1 d.66.1.4 PDB: 1h3e_A*	Back alignment and structure

>1fm0_D Molybdopterin convertin factor, subunit 1; molybdenum cofactor biosynthesis, transferase; 1.45A {Escherichia coli} SCOP: d.15.3.1 PDB: 1fma_D 1jw9_D 1jwa_D* 1jwb_D* 3bii_D 1nvi_D	Back alignment and structure

>2ktl_A Tyrosyl-tRNA synthetase; S4 fold, aminoacyl-tRNA synthetase, ligase; NMR {Aspergillus nidulans fgsc A4}	Back alignment and structure

>2jan_A Tyrosyl-tRNA synthetase; protein biosynthesis, aminoacyl-tRNA synthetase, tyrrs, ligase, tyrosine, RNA-binding, ATP-binding; 2.9A {Mycobacterium tuberculosis}	Back alignment and structure

>2ts1_A Tyrosyl-tRNA synthetase; ligase (synthetase); 2.30A {Geobacillus stearothermophilus} SCOP: c.26.1.1 PDB: 3ts1_A* 1tyd_E* 1tya_E* 1tyc_A 1tyb_E* 4ts1_A* 1jh3_A	Back alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Alignment Graph	Length	Definition	E-value
Query		240
d1v9fa_		250	d.265.1.3 (A:) Ribosomal large subunit pseudouridi	2e-20
d1v9ka_		227	d.265.1.3 (A:) Ribosomal large subunit pseudouridi	3e-12
d1vioa2		58	d.66.1.5 (A:0-57) Pseudouridine synthase RsuA N-te	1e-07
d1kska3		59	d.66.1.5 (A:1-59) Pseudouridine synthase RsuA N-te	4e-07
d1dm9a_		104	d.66.1.3 (A:) Heat shock protein 15 kD {Escherichi	4e-04

>d1v9fa_ d.265.1.3 (A:) Ribosomal large subunit pseudouridine synthase D, RluD {Escherichia coli [TaxId: 562]} Length = 250	Back information, alignment and structure


class: Alpha and beta proteins (a+b)
fold: Pseudouridine synthase
superfamily: Pseudouridine synthase
family: Pseudouridine synthase RsuA/RluD
domain: Ribosomal large subunit pseudouridine synthase D, RluD
species: Escherichia coli [TaxId: 562]

 Score = 84.6 bits (208), Expect = 2e-20
 Identities = 25/47 (53%), Positives = 37/47 (78%)

Query: 131 EAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCS 177
           E +DIPLDIVYED++++++NKP  +VVHP  GN  GT++N +LH+  
Sbjct: 2   EPQDIPLDIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLNALLHYYP 48

PyMOL of d1v9fa_

>d1v9ka_ d.265.1.3 (A:) Ribosomal large subunit pseudouridine synthase C, RluC {Escherichia coli [TaxId: 562]} Length = 227	Back information, alignment and structure

>d1vioa2 d.66.1.5 (A:0-57) Pseudouridine synthase RsuA N-terminal domain {Haemophilus influenzae [TaxId: 727]} Length = 58	Back information, alignment and structure

>d1kska3 d.66.1.5 (A:1-59) Pseudouridine synthase RsuA N-terminal domain {Escherichia coli [TaxId: 562]} Length = 59	Back information, alignment and structure

>d1dm9a_ d.66.1.3 (A:) Heat shock protein 15 kD {Escherichia coli [TaxId: 562]} Length = 104	Back information, alignment and structure

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Alignment Graph	Length	Definition	Probability
Query		240
d1v9fa_		250	Ribosomal large subunit pseudouridine synthase D,	99.82
d1v9ka_		227	Ribosomal large subunit pseudouridine synthase C,	99.73
d1vioa1		174	Ribosomal small subunit pseudouridine 516 synthase	99.48
d1kska4		172	Ribosomal small subunit pseudouridine 516 synthase	99.27
d1kska3		59	Pseudouridine synthase RsuA N-terminal domain {Esc	99.25
d1vioa2		58	Pseudouridine synthase RsuA N-terminal domain {Hae	99.23
d1dm9a_		104	Heat shock protein 15 kD {Escherichia coli [TaxId:	98.96
d1p9ka_		79	Hypothetical protein YbcJ {Escherichia coli [TaxId	98.85
d1c06a_		159	Ribosomal protein S4 {Bacillus stearothermophilus	98.36
d2gy9d1		204	Ribosomal protein S4 {Escherichia coli [TaxId: 562	98.2
d2uubd1		208	Ribosomal protein S4 {Thermus thermophilus [TaxId:	98.2
d1h3fa2		81	Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain	97.52
d1jh3a_		99	Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain	96.91
d1r3ea2		228	Pseudouridine synthase II TruB {Thermotoga maritim	95.8
d1k8wa5		242	Pseudouridine synthase II TruB {Escherichia coli [	95.74
d1sgva2		233	Pseudouridine synthase II TruB {Mycobacterium tube	95.39
d2ey4a2		245	Pseudouridine synthase II TruB {Archaeon Pyrococcu	94.77
d2apoa2		230	Pseudouridine synthase II TruB {Archaeon Methanoco	94.72

>d1v9fa_ d.265.1.3 (A:) Ribosomal large subunit pseudouridine synthase D, RluD {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

class: Alpha and beta proteins (a+b)
fold: Pseudouridine synthase
superfamily: Pseudouridine synthase
family: Pseudouridine synthase RsuA/RluD
domain: Ribosomal large subunit pseudouridine synthase D, RluD
species: Escherichia coli [TaxId: 562]

Probab=99.82  E-value=1.5e-21  Score=168.37  Aligned_cols=81  Identities=51%  Similarity=0.843  Sum_probs=68.4

Q ss_pred             cccCCCceeeecCCcEEEEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCC
Q 026355          131 EAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASI  210 (240)
Q Consensus       131 ~p~~~~l~Ilyed~~~lvvnKPaGl~v~p~~~~~~~Tl~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  210 (240)
                      .|++++++|||||+++||||||+||+|||+.++..+|+.+.|..++...                           ....
T Consensus         2 ~P~~~~l~IlyeD~~~ivvnKP~gl~~hp~~~~~~~t~~~~l~~~~~~~---------------------------~~~~   54 (250)
T d1v9fa_           2 EPQDIPLDIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLNALLHYYPPI---------------------------ADVP   54 (250)
T ss_dssp             CCCCCCCCEEEECSSEEEEEECSSCCSSCBTTBSSSSHHHHHHHHCGGG---------------------------GGSG
T ss_pred             CCCCCCCCEEEECCCEEEEECCCCCCCcCCCCCCCccHHHHHHHHhhhc---------------------------cCCC
Confidence            4678889999999999999999999999999888899999999876310                           0124


Q ss_pred             CccccCcCCCCCceEEEeecCCccccCC
Q 026355          211 RPGIVHRLDKGTSGLLVVAKVIFSPFGN  238 (240)
Q Consensus       211 ~~~~VhRLDr~TSGLLl~ak~~~aa~~~  238 (240)
                      .+++|||||++|||||||||+.+++..+
T Consensus        55 ~~~~vHRLDr~TSGlll~Ak~~~a~~~l   82 (250)
T d1v9fa_          55 RAGIVHRLDKDTTGLMVVAKTVPAQTRL   82 (250)
T ss_dssp             GGGBCCCCCTTCEEEEEEESSHHHHHHH
T ss_pred             ceeEEeecCCCCcceEEEecccHHHHhh
Confidence            5678999999999999999999887643

PyMOL of d1v9fa_

>d1v9ka_ d.265.1.3 (A:) Ribosomal large subunit pseudouridine synthase C, RluC {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d1vioa1 d.265.1.3 (A:58-231) Ribosomal small subunit pseudouridine 516 synthase RsuA {Haemophilus influenzae [TaxId: 727]}	Back information, alignment and structure

>d1kska4 d.265.1.3 (A:60-231) Ribosomal small subunit pseudouridine 516 synthase RsuA {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d1kska3 d.66.1.5 (A:1-59) Pseudouridine synthase RsuA N-terminal domain {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d1vioa2 d.66.1.5 (A:0-57) Pseudouridine synthase RsuA N-terminal domain {Haemophilus influenzae [TaxId: 727]}	Back information, alignment and structure

>d1dm9a_ d.66.1.3 (A:) Heat shock protein 15 kD {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d1p9ka_ d.66.1.6 (A:) Hypothetical protein YbcJ {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d1c06a_ d.66.1.2 (A:) Ribosomal protein S4 {Bacillus stearothermophilus [TaxId: 1422]}	Back information, alignment and structure

>d2gy9d1 d.66.1.2 (D:2-205) Ribosomal protein S4 {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d2uubd1 d.66.1.2 (D:2-209) Ribosomal protein S4 {Thermus thermophilus [TaxId: 274]}	Back information, alignment and structure

>d1h3fa2 d.66.1.4 (A:352-432) Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain {Thermus thermophilus [TaxId: 274]}	Back information, alignment and structure

>d1jh3a_ d.66.1.4 (A:) Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain {Bacillus stearothermophilus [TaxId: 1422]}	Back information, alignment and structure

>d1r3ea2 d.265.1.2 (A:10-237) Pseudouridine synthase II TruB {Thermotoga maritima [TaxId: 2336]}	Back information, alignment and structure

>d1k8wa5 d.265.1.2 (A:9-250) Pseudouridine synthase II TruB {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d1sgva2 d.265.1.2 (A:3-235) Pseudouridine synthase II TruB {Mycobacterium tuberculosis [TaxId: 1773]}	Back information, alignment and structure

>d2ey4a2 d.265.1.2 (A:8-252) Pseudouridine synthase II TruB {Archaeon Pyrococcus furiosus [TaxId: 2261]}	Back information, alignment and structure

>d2apoa2 d.265.1.2 (A:17-246) Pseudouridine synthase II TruB {Archaeon Methanococcus jannaschii [TaxId: 2190]}	Back information, alignment and structure